[gmx-users] Genbox problem ...

[Kedar Potdar]

Yeah actually I got cause of the problem... :)

I need to remove the "topinput" file before renaming "TEMP_FILENM" with "
topinput".

Thanks...

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of David van der Spoel
Sent: Tuesday, May 29, 2007 6:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Genbox problem ...

Kedar Potdar wrote:
> Hi friends,
> 
>  
> 
> I have compiled Gromacs on native windows. The first two program in demo 
> script (perl implementation of script "demo") work fine but genbox 
> displays following output
> 
>  
> 
> Reading solute configuration
> 
> Glycine aRginine prOline Methionine Alanine Cystine Serine
> 
> Containing 145 atoms in 13 residues
> 
> Initialising van der waals distances...
> 
> Reading solvent configuration
> 
> "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
> 
> solvent configuration contains 648 atoms in 216 residues
> 
>  
> 
> Initialising van der waals distances...
> 
> Will generate new solvent configuration of 2x2x2 boxes
> 
> Generating configuration
> 
> Sorting configuration
> 
> Found 1 molecule type:
> 
>     SOL (   3 atoms):  1728 residues
> 
> Calculating Overlap...
> 
> box_margin = 0.315
> 
> Removed 2895 atoms that were outside the box
> 
> Succesfully made neighbourlist
> 
> nri = 11448, nrj = 456822
> 
> Checking Protein-Solvent overlap: tested 4131 pairs, removed 228 atoms.
> 
> Checking Solvent-Solvent overlap: tested 36954 pairs, removed 597 atoms.
> 
> Added 488 molecules
> 
> Generated solvent containing 1464 atoms in 488 residues
> 
> Writing generated configuration to cpeptide_b4em.gro
> 
> Glycine aRginine prOline Methionine Alanine Cystine Serine
> 
>  
> 
> Output configuration contains 1609 atoms in 501 residues
> 
> Volume                 :     17.1176 (nm^3)
> 
> Density                :     1002.99 (g/l)
> 
> Number of SOL molecules:    488
> 
>  
> 
> Processing topology
> 
>  
> 
> Back Off! I just backed up cpeptide.top to ./#cpeptide.top.1#
> 
>  
> 
> *Cpeptide.top file is of zero bytes now. and all further programs in the 
> test fail after this.*
> 
> * *
> 
> Has anybody faced such problem before? What is remedy for this problem?
> 
Check the source code for opening of the file in genbox. It tries to 
append to the file, and the code for that may be different windows than 
under Unix.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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